Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing

Abstract Soils represent one of the largest and most active pools of C in the biosphere, and soil respiration represents a major component of global C flux. Fungi are essential to soil carbon cycling due to their propensity for decomposing organic polymers such as cellulose. We performed high throughput sequencing enabled stable isotope probing (HTS-SIP) with 13 C-cellulose to characterize the dynamics of fungi and bacteria during cellulose degradation in an agricultural soil. A total of 1900 fungal taxa were observed and 190 of these assimilated 13 C-cellulose during a 30-day incubation. A majority of 13 C-labeled fungi belonged to Ascomycota , Basidiomycota , and Mucoromycota . However, most 13 C-labeled fungi could not be annotated at the species (71%, n  = 134), or genus (49%, n  = 93) level. Mucoromycota were 13 C-labeled early, and by day 3 the most abundant 13 C-labeled organism belonged to Mortierella . In contrast, 13 C-labeled Ascomycota increased in diversity through day 14 and their relative abundance comprised more than 40% of fungal ITS sequences by day 30. These results show that: i ) the majority of fungal taxa that assimilated 13 C from 13 C-cellulose are uncultivated and poorly characterized, ii ) the beta-diversity of 13 C-labeled fungi changed significantly over time during cellulose degradation, iii ) a relatively small number of the 13 C-labeled taxa dominated the community response to cellulose, and iv ) fungi incorporated cellulose into DNA more rapidly and in greater numbers than did bacteria. These results show that fungi in a tilled agricultural field respond rapidly to new cellulose inputs, exhibiting complex temporal dynamics that likely drive carbon flow into diverse taxa within the soil community.